Spatial_cluster: Plotting clusters of cells by choosing between 10X Genomics...

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Plotting clusters of cells by choosing between 10X Genomics clustering or reclustering the cells.

Description

Plotting clusters of cells by choosing between 10X Genomics clustering or reclustering the cells.

Usage

Spatial_cluster(
  cluster = c("GEX_cluster", "reclustering"),
  GEX.out.directory.list,
  vgm_VDJ,
  vgm_cluster,
  sample_names,
  bcs_merge,
  images_tibble,
  title,
  size,
  legend_title
)

Arguments

cluster	Character vector to describe the clustering, "GEX_cluster" is for plotting 10X Genomics clustering and "reclustering" is for reclustering the cells according to the given subset.
GEX.out.directory.list	Character vector that give the path to filtered_feature_bc_matrix data.
vgm_VDJ	Data frame containing cell of interest and x and y coordinates and GEX_barcode.
vgm_cluster	Data frame containing GEX barcode and cluster given by 10X Genomics. Only needed if cluster parameter is set to "GEX_cluster".
sample_names	Character vector containing the name of the sample.
bcs_merge	Data frame containing imagerow, imagecol and barcode of the cells belonging to the spatial image. It can also be created by the function scaling_spatial_image_parameter by selecting the output parameter 10.
images_tibble	Tbl-df containing the sample name, grob, height and width of the spatial image. It can also be created by the function scaling_spatial_image_parameter by selecting the output parameter 5.
title	Character vector to name the plot.
size	Number, to define the size of the text, default = 15.
legend_title	Character vector to name the legend scale.

Value

If plotting = TRUE, returns a list containing [[1]] the plot of the selected cells according to their group, [[2]] a data frame that contains the column seurat_clusters with the new cluster. If plotting = FALSE, it returns just the data frame.

Examples

## Not run: 
#Clustering of whole cells regardless of cell type
GEX_cluster_B_cells<-Spatial_cluster(cluster = "GEX_cluster",
vgm_cluster = vgm_with_simulated_VDJ$spatial$cluster[[1]],
vgm_VDJ = vgm_with_simulated_VDJ$VDJ,
GEX.out.directory.list = GEX.out.directory.list[[1]],images_tibble=scaling_parameters[[5]],
bcs_merge=scaling_parameters[[10]], title = "B cells",
sample_names = sample_names, legend_title = "GEX clusters" )
GEX_cluster_B_cells[[1]]

#Reclustering with only B cells
reclustering_B_cells<-Spatial_cluster(cluster = "reclustering",
vgm_VDJ = vgm_with_simulated_VDJ$VDJ,
GEX.out.directory.list = GEX.out.directory.list[[1]],
images_tibble=scaling_parameters[[5]],bcs_merge=scaling_parameters[[10]],
title = "B cells", sample_names = sample_names, legend_title = "Reclustering")
reclustering_B_cells[[1]]

## End(Not run)

Platypus documentation built on Aug. 15, 2022, 9:08 a.m.